It's Complicated
by 84-Quill-72
Summary: Holly and Artemis begin to develop a different relationship and find that as simple as it seems, it starts to complicate their day to day lives. *Root is alive and there has been an extensive backstory created for him.* Rated M for later chapters.
1. Chapter 1

Chapter One

Artemis was too busy plotting dastardly acts to check his cell phone. Actually he was busy entertaining his twin brothers Myles and Beckett in the sense of being tackled and pinned for the fifteenth or twentieth time-he had lost count. But that didn't sound very criminal mastermind like.

Artemis allowed himself a small smile as he watched his brothers run to their father holding his cell phone high in the air signalling victory.

He and his family were spending the weekend at their lake house on Lough Ree. Today was Sunday and they had to return to the manor before Butler worried himself to pieces.

As Artemis neared his family he realized that not only was he enjoying himself, but he hadn't thought of Holly all weekend. This was quite an accomplishment as for the past two months the only thought that had not been about the little elf was the one concerning Artemis's strong distaste of liver.

The young Irish boy had no idea why his friend was on his mind so often lately but he didn't like it. It felt weird, almost like kissing a girl who was like your sister in every way except blood. Artemis and Holly had a special relationship and whenever they were together, Artemis always wanted to slow time down because it always seemed they never had enough.

He sighed deeply as his mother's mere mention of wanting nutmeg hot chocolate when they got home had Artemis thinking of Holly's soft, nut-brown skin. He knew that the rest of the summer was going to be filled with days like this one and he had no one to talk to about it.

Holly Short of the L.E.P. was sitting at her desk doing paperwork while she anxiously waiting for Artemis to answer the message she had sent him. She was amazed at how their relationship had changed over the years. In the beginning she had hated him, now, not even seven years later, she and Artemis could talk for eight hours straight-at the very least.

She looked at her human cell phone and frowned; still no reply. She checked her desk clock and saw that it had been two hours since she had sent the message. Holly was contemplating sending another one but Julius Root and Trouble Kelp walked up behind her.

"What's going on Short?" Trouble asked looking at her phone. "Trying to get a hold of your dear, sweet little Mud Man?" He winked playfully at her but didn't see the glare she shot him. It was the one that Holly Short was famous for; the glare that could have killed the entire Nazi Party from five feet away had Holly been there in World War 2.

"Commander," Holly started, ignoring Trouble completely, "I'm requesting an extended leave of absence."

That one sentence took all who were within earshot by such surprise that some of them had to sit down. All those left standing had to either grab onto a wall, a chair, or someone standing close to them to ensure that they themselves didn't fall down.

Root looked just as taken aback as the rest of the room but he didn't show it, "For how long?"

Holly looked at him and smiled wearily, "Two months at the least."

"Two months? Short what in Frond's name brought this on?"

Holly sighed sounding exhausted, "Oh, I don't know maybe it was lack of sleep, lack of proper food, or maybe it was the lack of respect from anyone that even remembers the Fowl incidents." She snapped out the last statement with such malice that Root took a step back.

"Holly, everyone here respects you; not to mention how grateful most of them are that you were involved in the Fowl incidents." Root sighed and put a hand on Holly's shoulder, "If it hadn't been for you the People and the Mud Men would be at war right now."

"Those grateful ones are those who know only that I helped crush a rebellion and assisted in the mind-wiping of an innocent teenage boy. And yes Julius, that last one is definitely something that I want to be remembered for." She shook her head and looked him straight in the eyes, "I am requesting a two month leave of absence; and if you don't give it to me I'll go directly to the Council. I'm sure that they will be happy to oblige me, don't you think?"

"Holly that's not fair," Trouble said looking at her, "Everybody knows that the Council would love to be rid of you; if you go to them, well, they just might make your leave of absence permanent."

Holly looked at him and laughed coldly, "Trouble, do you honestly think that I care? Right now all I want is a two month leave of absence to explore other job options. That's it. I'll come back, eventually. Maybe."

The commander looked at her, sighed in resignation, and nodding, walked to his office to do the paperwork. Julius closed his office door and sat behind his desk shaking his head. _Why on earth do you want to leave? _He thought to himself, He had handpicked Holly Short to be the first female on his team because when he looked in her eyes he saw something that the other women hadn't had: passion; the will to work the hardest, to prove herself.

If Artemis Fowl hadn't come along, Holly would be the one up for the promotion right now instead of Trouble. _Strange, _He thought, _to think that I'd prefer _Commander Holly Short_ to _Commander Trouble Kelp_. _

There had only been one thing that had scared him about Holly, the fact that she was the daughter of the woman he had once been married to; Coral Short, a member of the LEPmarine. It had hit him hard when she died, he had loved her. The reason he left had been to keep her safe.

Despite all that he had remained true to the vows he gave Coral on their wedding day, he hadn't taken another woman, hell, he hadn't looked at another woman, he hadn't wanted to. Now when he thought of Holly, he wondered who her father was, there was nothing on record and it had never once occurred to him that he could be her father.

He stopped what he was doing when he thought that he could be her father. _That can't be possible, can it? Coral and I weren't together long enough to have a child. _Root paused, _Were we? _


	2. Chapter 2

Chapter Two

Foaly burst into his office, "Darvit Julius! You can't let an elf like Holly slip through your fingers like this." The centaur was glaring at him and for some reason Root felt like his life was actually in danger.

"Julius, if you sign that form allowing Holly to walk out that door you're going to find another one on your desk tomorrow informing you that I'm never walking back through it." Foaly inhaled deeply and glared murderously at Root.

Root sighed and looked at the centaur. "Foaly, I don't want her to go either but if I don't sign this form she'll just go to the Council and they'll make it so that she can't come back - ever." He looked down at the one lonely picture frame on his desk and shook his head. "She'll come back Foaly; she just needs to get this out of her system. She's feeling tired and alone and if going on a soul search is her way of coping, then we have to let her go."

"But...but" The centaur sputtered before nodding "I know it's just -"

"It's just what?" Root asked, suspicion darkening his eyes as he stared at Foaly.

"You do know that she's just going to run to _him_ right?" The centaur finished quietly, looking anywhere but Root's face. Julius hated the relationship that had evolved between his officer and the young Mud Man over the years but he had no grounds upon which to prevent Holly from seeing him.

Julius had just finished the paperwork for Holly when she walked into his office, dressed in civies and holding a visa.

"Hi, I was just coming to check if you'd finished my papers." Holly said avoiding his gaze; she felt horrible for doing this to Root but she was sick of the looks she got; she had to see if there was another way for her to get through the day or if there was something else she could do for her career.

"Just finished them." He said and stood, handing them to her over the desk "May I ask what your plans are?" He asked nodding to the visa in her hand.

She shrugged "I'm going to take in some fresh, unfiltered air above ground for a few days." She took the papers and slipped them into her bag along with the visa.

"Anywhere near Fowl Manor?" He asked gruffly, grabbing another stack of papers to go through.

Holly's eyes flashed as her head snapped up to look at her commanding officer "I don't think that's any of your business. Sir."

"True, but I like to know where my officers are in case I need to reach them."

"You have other officers you can contact if anything goes wrong." She muttered, trying not to let her anger show.

Root just barely heard the comment and given the circumstances, let it slide; he wasn't going to be the thing that drove Holly out the door for good. "Well everything seems to be in order. I hope you find what you're looking for Holly I really do."

"Thank you sir." She choked the words out, feeling even worse than she had moments before.

"Oh and Short, try to refrain from saving the world with Fowl this time." He grumbled taking out a fungus cigar.

"So would you rather I let the world end?" Holly asked although she knew that she wasn't going to get a response. He shook her head and sighed "I'm sorry about this Commander, I just need to figure out if this is really what I want to do.."

Root said nothing as she walked out of his office; he knew how demanding the job was especially if you were tied to a case or person that no one was about to forget anytime soon so he couldn't begrudge her attempt to find something else.

* * *

Holly inhaled deeply as she stepped into the Irish countryside; she had about a half hour walk to Fowl Manor and then another hour of explaining why she was there to Artemis. Despite all the issues that had surfaced that day, Holly was happy to be above ground and excited to see Artemis and the others again. It had been a long time since their last round at saving the world.

Eventually Holly found herself wandering up the long driveway of Fowl Manor; as she came up to the door, she braced herself for the questions that would be thrown at her, especially if his parents were home.

She had barely knocked when the door flew open and she was pulled into the grand foyer. "What the - ?"

"Shh." Artemis said as he quickly but quietly tried to pull her upstairs "I'm sorry I didn't get back to you but why are you here?" He whispered throwing a glance at the door that led to the parlour.

"I took some time off of work and thought I'd drop by like I usually do. Why are we whispering?" She whispered back to him.

"Because Arty probably didn't want us to know we had company." A melodic voice said from behind them. The couple froze and slowly turned around to face Artemis Senior and Angeline both of whom were regarding them with curious looks.

"See Angeline? I told you there was nothing to worry about." Artemis Senior said to his wife. "She's quite the catch son." He winked at the younger and it dawned on Holly and "Arty" that his parents thought she was his girlfriend.

"What's her name sweetheart?" Angeline asked ignoring her husbands comment. She was studying Holly closely, wondering where Arty had found such an exotic beauty.

Holly shifted a little under the gaze of the woman. She nudged Artemis knowing that while it wasn't great for them to be thought of as dating, it would be better than trying to explain who she _really _was.

"Mother, father, I'd like you to meet Holly Short... My girlfriend." Artemis said feeling thoroughly awkward, especially when Butler and Juliet came out of the parlour just in time to hear the last part of the statement.

"A pleasure to meet you Holly." Artemis Sr. said giving her a harming version of Artemis' signature vampire smile.

"So tell us my dear," Angeline began as she led Holly back into the parlour followed by Artemis and his father. "How did you and Artemis meet?"

Holly's eyes widened and she shot a look over to Artemis, her hazel and blue eyes begging for help.


End file.
